If you do not mind jumping down in to terminal, then this is pretty darn easy. If you are in
/Users/username, which is your $HOME directory and there is a subdirectory named foo that you want to zip but ignore all .DS_Store files, then do the following:
zip -r foo.zip foo -x "*.DS_Store"
To interpret this, we are running the zip executable with the following parameters/arguments:
-r for recursively including all directories underneath the targets we want to zip.
foo.zip is the name of the zip archive we are creating
foo is the target directory we want to zip up
-x "*.DS_Store" excludes all files whose path ends in the string ".DS_Store"
No goofy third party applications needed nor do you need to trash your .DS_Store files at all - just rely on all of the unix tool goodness built right in to OSX / Darwin.